diff --git a/denv_pipeline/utils/set_up_scripts.py b/denv_pipeline/utils/set_up_scripts.py
index 6281b74..eda5f06 100644
--- a/denv_pipeline/utils/set_up_scripts.py
+++ b/denv_pipeline/utils/set_up_scripts.py
@@ -101,6 +101,9 @@ def symlink_setup(config, cwd):
 
     symlink = config["symlink"]
     
+    if not os.path.exists(config["indir"]):
+        misc.make_directory(config["indir"])
+
     os.chdir(config["indir"])
     os.system(f"ycgaFastq {symlink}")
     os.chdir(cwd)